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Chinnam NB, Thapar R, Arvai AS, Sarker AH, Soll JM, Paul T, Syed A, Rosenberg DJ, Hammel M, Bacolla A, Katsonis P, Asthana A, Tsai MS, Ivanov I, Lichtarge O, Silverman RH, Mosammaparast N, Tsutakawa SE, Tainer JA. ASCC1 structures and bioinformatics reveal a novel Helix-Clasp-Helix RNA-binding motif linked to a two-histidine phosphodiesterase. J Biol Chem 2024; 300:107368. [PMID: 38750793 DOI: 10.1016/j.jbc.2024.107368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024] Open
Abstract
Activating signal co-integrator complex 1 (ASCC1) acts with ASCC-ALKBH3 complex in alkylation damage responses. ASCC1 uniquely combines two evolutionarily ancient domains: nucleotide-binding K-Homology (KH) (associated with regulating splicing, transcriptional, and translation) and two-histidine phosphodiesterase (PDE) (associated with hydrolysis of cyclic nucleotide phosphate bonds). Germline mutations link loss of ASCC1 function to spinal muscular atrophy with congenital bone fractures 2 (SMABF2). Herein analysis of The Cancer Genome Atlas (TCGA) suggests ASCC1 RNA overexpression in certain tumors correlates with poor survival, Signatures 29 and 3 mutations, and genetic instability markers. We determined crystal structures of Alvinella pompejana (Ap) ASCC1 and Human (Hs) PDE domain revealing high resolution details and features conserved over 500 million years of evolution. Extending understanding of the KH domain Gly-X-X-Gly sequence motif, we define a novel structural Helix-Clasp-Helix (HCH) nucleotide binding motif and show ASCC1 sequence-specific binding to CGCG-containing RNA. The V-shaped PDE nucleotide binding channel has two His-Φ-Ser/Thr-Φ (HXT) motifs (Φ being hydrophobic) positioned to initiate cyclic phosphate bond hydrolysis. A conserved atypical active-site histidine torsion angle implies a novel PDE substrate. Flexible active site loop and arginine-rich domain linker appear regulatory. Small angle X-ray scattering (SAXS) revealed aligned KH-PDE RNA binding sites with limited flexibility in solution. Quantitative evolutionary bioinformatic analyses of disease and cancer-associated mutations support implied functional roles for RNA binding, phosphodiesterase activity, and regulation. Collective results inform ASCC1 roles in transactivation and alkylation damage responses, its targeting by structure-based inhibitors, and how ASCC1 mutations may impact inherited disease and cancer.
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Affiliation(s)
- Naga Babu Chinnam
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, United States
| | - Roopa Thapar
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, United States
| | - Andrew S Arvai
- Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, United States
| | - Altaf H Sarker
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jennifer M Soll
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University in St. Louis, St. Louis, MO 63110, United States
| | - Tanmoy Paul
- Department Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302 United States
| | - Aleem Syed
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, United States
| | - Daniel J Rosenberg
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, United States
| | - Panagiotis Katsonis
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, United States
| | - Abhishek Asthana
- Department Cancer Biology, Cleveland Clinic Foundation, Lerner Research Institute, Cleveland, OH, 44195, United States
| | - Miaw-Sheue Tsai
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Ivaylo Ivanov
- Department Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302 United States
| | - Olivier Lichtarge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, United States
| | - Robert H Silverman
- Department Cancer Biology, Cleveland Clinic Foundation, Lerner Research Institute, Cleveland, OH, 44195, United States
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University in St. Louis, St. Louis, MO 63110, United States
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States.
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2
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Decio A, Giorda R, Panzeri E, Bassi MT, D'Angelo MG. Clinical phenotype and next-generation sequencing as essential tools for the diagnosis of a rare form of congenital myopathy due to a TRIP4 intragenic deletion. Neurol Sci 2024; 45:819-823. [PMID: 37792112 DOI: 10.1007/s10072-023-07102-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 09/26/2023] [Indexed: 10/05/2023]
Affiliation(s)
- Alice Decio
- Unit of Rehabilitation of Rare Diseases of the Central and Peripheral Nervous System, Scientific Institute IRCCS E. Medea, Via Don L. Monza 20, 23842, Bosisio Parini (LC), Italy.
| | - Roberto Giorda
- Molecular Biology Laboratory, IRCCS Eugenio Medea, Bosisio Parini (LC), Italy
| | - Elena Panzeri
- Molecular Biology Laboratory, IRCCS Eugenio Medea, Bosisio Parini (LC), Italy
| | - Maria Teresa Bassi
- Molecular Biology Laboratory, IRCCS Eugenio Medea, Bosisio Parini (LC), Italy
| | - Maria Grazia D'Angelo
- Unit of Rehabilitation of Rare Diseases of the Central and Peripheral Nervous System, Scientific Institute IRCCS E. Medea, Via Don L. Monza 20, 23842, Bosisio Parini (LC), Italy
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Frongia I, Spagnoli C, Rizzi S, Frattini D, Leon A, Caraffi SG, Pollazzon M, Garavelli L, Pisani F, Fusco C. 'A novel TRIP4 Variant Associated with Peripheral Neuropathy: Expanding the Clinical and Genetic Spectrum of ASC1-Related Myopathy'. J Neuromuscul Dis 2024; 11:213-219. [PMID: 38143368 PMCID: PMC10789366 DOI: 10.3233/jnd-230110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2023] [Indexed: 12/26/2023]
Abstract
Activating Signal Cointegrator 1 complex (ASC-1 complex) is a ribonucleoprotein tetramer participating in transcriptional coactivation and RNA processing, consisting of four subunits: ASCC1-ASCC3 and ASC-1. Pathogenic variants in the TRIP4 and ASCC1 genes, encoding the ASC-1 and ASCC1 subunits, were recently described in congenital myopathic conditions without signs of motor neuron involvement, and Spinal Muscular Atrophy-like (SMA-like) phenotype with prenatal bone fractures. We present a novel pathogenic TRIP4 variant in two siblings with severe phenotype and mixed sensory-motor polyneuropathy. The reviewed phenotypic spectrum is broad, but sensory-motor polyneuropathy is so-far unreported. We thus expand ASC-1 related myopathy phenotype.
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Affiliation(s)
- Ivana Frongia
- Struttura Complessa di Neuropsichiatria Infantile, Dipartimento Materno-Infantile, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Carlotta Spagnoli
- Struttura Complessa di Neuropsichiatria Infantile, Dipartimento Materno-Infantile, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Susanna Rizzi
- Struttura Complessa di Neuropsichiatria Infantile, Dipartimento Materno-Infantile, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Daniele Frattini
- Struttura Complessa di Neuropsichiatria Infantile, Dipartimento Materno-Infantile, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | | | - Stefano Giuseppe Caraffi
- Struttura Complessa di Genetica Medica, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Marzia Pollazzon
- Struttura Complessa di Genetica Medica, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Livia Garavelli
- Struttura Complessa di Genetica Medica, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Francesco Pisani
- Child Neuropsychiatric Unit, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Carlo Fusco
- Struttura Complessa di Neuropsichiatria Infantile, Dipartimento Materno-Infantile, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
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Victor AK, Hedgecock T, Donaldson M, Johnson D, Rand CM, Weese-Mayer DE, Reiter LT. Analysis and comparisons of gene expression changes in patient- derived neurons from ROHHAD, CCHS, and PWS. Front Pediatr 2023; 11:1090084. [PMID: 37234859 PMCID: PMC10206321 DOI: 10.3389/fped.2023.1090084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Background Rapid-onset obesity with hypothalamic dysfunction, hypoventilation, and autonomic dysregulation (ROHHAD) syndrome is an ultra-rare neurocristopathy with no known genetic or environmental etiology. Rapid-onset obesity over a 3-12 month period with onset between ages 1.5-7 years of age is followed by an unfolding constellation of symptoms including severe hypoventilation that can lead to cardiorespiratory arrest in previously healthy children if not identified early and intervention provided. Congenital Central Hypoventilation syndrome (CCHS) and Prader-Willi syndrome (PWS) have overlapping clinical features with ROHHAD and known genetic etiologies. Here we compare patient neurons from three pediatric syndromes (ROHHAD, CCHS, and PWS) and neurotypical control subjects to identify molecular overlap that may explain the clinical similarities. Methods Dental pulp stem cells (DPSC) from neurotypical control, ROHHAD, and CCHS subjects were differentiated into neuronal cultures for RNA sequencing (RNAseq). Differential expression analysis identified transcripts variably regulated in ROHHAD and CCHS vs. neurotypical control neurons. In addition, we used previously published PWS transcript data to compare both groups to PWS patient-derived DPSC neurons. Enrichment analysis was performed on RNAseq data and downstream protein expression analysis was performed using immunoblotting. Results We identified three transcripts differentially regulated in all three syndromes vs. neurotypical control subjects. Gene ontology analysis on the ROHHAD dataset revealed enrichments in several molecular pathways that may contribute to disease pathology. Importantly, we found 58 transcripts differentially expressed in both ROHHAD and CCHS patient neurons vs. control neurons. Finally, we validated transcript level changes in expression of ADORA2A, a gene encoding for an adenosine receptor, at the protein level in CCHS neurons and found variable, although significant, changes in ROHHAD neurons. Conclusions The molecular overlap between CCHS and ROHHAD neurons suggests that the clinical phenotypes in these syndromes likely arise from or affect similar transcriptional pathways. Further, gene ontology analysis identified enrichments in ATPase transmembrane transporters, acetylglucosaminyltransferases, and phagocytic vesicle membrane proteins that may contribute to the ROHHAD phenotype. Finally, our data imply that the rapid-onset obesity seen in both ROHHAD and PWS likely arise from different molecular mechanisms. The data presented here describes important preliminary findings that warrant further validation.
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Affiliation(s)
- A. Kaitlyn Victor
- IPBS Program, Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Tayler Hedgecock
- IPBS Program, Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Martin Donaldson
- Department of Pediatric Dentistry and Community Oral Health, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Daniel Johnson
- Molecular Bioinformatics Core, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Casey M. Rand
- Department of Pediatrics, Division of Autonomic Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago and Stanley Manne Children’s Research Institute, Chicago, IL, United States
| | - Debra E. Weese-Mayer
- Department of Pediatrics, Division of Autonomic Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago and Stanley Manne Children’s Research Institute, Chicago, IL, United States
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Lawrence T. Reiter
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, United States
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Sharova M, Guseva D, Kurenkov A, Novoselova O, Murtazina A, Skoblov M. Congenital myopathy as a new phenotype caused by two undescribed variants in ASCC1 gene. Am J Med Genet A 2022; 188:3100-3105. [PMID: 35838082 DOI: 10.1002/ajmg.a.62898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 05/19/2022] [Accepted: 06/02/2022] [Indexed: 01/31/2023]
Abstract
We present a patient with congenital myopathy and an inborn epiphysiolysis of the ulna. Whole-exome sequencing analysis revealed two novel mutations in Activation Signal Cointegrator Complex 1 (ASCC1) gene in a compound heterozygous state-a splicing variant c.395-2A>G and a deletion of the first two coding exons. Homozygous and compound heterozygous LoF variants in ASCC1 gene lead to a severe phenotype of spinal muscular atrophy with congenital bone fractures 2 (SMABF2). All patients described to date presented with a severe muscular hypotony, inborn fractures, and passed away shortly after birth while our proband had moderate hypotony, no fractures, but epiphysiolysis and he was 3.5 years old at the time of examination. To explain the phenotype of our patient, we performed an RNA analysis of all family members. We discovered that the c.395-2A>G variant results in two aberrant mRNA isoforms. We also validated the deletion of two exons in ASCC1 gene that lead to the increased expression of this truncated transcript by 1.8 times. To investigate the possible impact of this deletion on the phenotype we predicted a new Kozak sequence in exon 4 that could lead to the formation of a truncated protein with shortened KH domain and a full RNA ligase-like domain. We suggest that this unexpectedly different phenotype of the proband with ASCC1-related disorder could be explained by the presence of the truncated protein with an increased expression.
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Affiliation(s)
| | - Darya Guseva
- Research Centre for Medical Genetics, Moscow, Russia
| | - Alexey Kurenkov
- National Medical Research Center for Children's Health, the Russian Federation Ministry of Healthcare, Moscow, Russia
| | - Olga Novoselova
- Genomed Ltd., Genetic Diagnostic Lab, Moscow, Russia.,Filatov N.F. Children's City Hospital 103001, Moscow, Russia
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Marais A, Bertoli-Avella AM, Beetz C, Altunoglu U, Alhashem A, Mohamed S, Alghamdi A, Willems P, Tsoutsou E, Fryssira H, Pons R, Almarzooq R, Karatoprak EY, Ayaz A, Ünverengil G, Calvo M, Yüksel Z, Bauer P. Further clinical and genetic evidence of ASC-1 complex dysfunction in congenital neuromuscular disease. Eur J Med Genet 2022; 65:104537. [PMID: 35690317 DOI: 10.1016/j.ejmg.2022.104537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 05/21/2022] [Accepted: 06/06/2022] [Indexed: 11/03/2022]
Abstract
Transcriptional coregulators modulate the efficiency of transcription factors. Bi-allelic variants in TRIP4 and ASCC1, two genes that encode members of the tetrameric coregulator ASC-1, have recently been associated with congenital bone fractures, hypotonia, and muscular dystrophy in a total of 22 unrelated families. Upon exome sequencing and data repository mining, we identified six new patients with pathogenic homozygous variants in either TRIP4 (n = 4, two novel variants) or ASCC1 (n = 2, one novel variant). The associated clinical findings confirm and extend previous descriptions. Considering all patients reported to date, we provide supporting evidence suggesting that ASCC1-related disease has a more severe phenotype compared to TRIP4-related disorder regarding higher incidence of perinatal bone fractures and shorter survival.
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Affiliation(s)
| | | | | | - Umut Altunoglu
- Department of Medical Genetics, Koç University, School of Medicine, 34450, Istanbul, Turkey
| | - Amal Alhashem
- Division of Genetics and Metabolic Medicine, Department of Pediatrics, Prince Sultan Military Medical City Riyadh, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Sarar Mohamed
- Division of Genetics and Metabolic Medicine, Department of Pediatrics, Prince Sultan Military Medical City Riyadh, Saudi Arabia; Prince Abdullah Bin Khaled Coeliac Disease Research Chair, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Department of Pediarics, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Abdulaziz Alghamdi
- Pediatrics Department, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | | | - Eirini Tsoutsou
- Medical Genetics Department, Choremio Research Laboratory, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Greece
| | - Helena Fryssira
- Medical Genetics Department, Choremio Research Laboratory, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Greece
| | - Roser Pons
- Medical Genetics Department, Choremio Research Laboratory, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Greece
| | - Reem Almarzooq
- Pediatric Department, Salmaniya Medical Complex, Manama, Bahrain
| | - Elif Yüksel Karatoprak
- Departments of Pediatric Neurology, İstanbul Medeniyet University Faculty of Medicine, Göztepe Training and Research Hospital, İstanbul, Turkey
| | - Akif Ayaz
- Istanbul Medipol University Faculty of Medicine, Department of Medical Genetics, Istanbul, Turkey
| | - Gökçen Ünverengil
- Department of Pathology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
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ASC1 complex related conditions: Two novel paediatric patients with TRIP4 pathogenic variants and review of literature. Eur J Med Genet 2022; 65:104469. [PMID: 35276412 DOI: 10.1016/j.ejmg.2022.104469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 01/11/2022] [Accepted: 02/25/2022] [Indexed: 11/22/2022]
Abstract
Pathogenic variants in the genes encoding for the ASC1 complex were recently reported in patients with congenital fractures, joint contractures, neonatal hypotonia and respiratory distress. Here we report two male children with biallelic TRIP4 pathogenic loss of function variants. The first child presented with foetal bradykinesia, neonatal respiratory distress, central and peripheral hypotonia, constipation, hyperlaxity, left uretero-hydronephrosis and post-obstructive kidney dysplasia. The second had severe central and peripheral neonatal hypotonia, feeding difficulties, kyphosis, developmental delay and hyperlaxity. Detailed review of all reported cases with ASCC1 (12 patients) and TRIP4 (18 patients) variants highlights striking genotype-phenotype correlations. This is the fourth report of patients with TRIP4 variants and the first description of post-obstructive kidney dysplasia in this condition.
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